2603.00245 RT-qPCR Primer Design: Highly Specific Primer Design for mRNA Detection with Homolog Discrimination
This skill provides a rigorous workflow for designing specific RT-qPCR primers that can distinguish between highly similar gene family members (e.g., DDX3X vs DDX3Y) and prevent genomic DNA contamination. The workflow includes sequence acquisition, homolog alignment, exon mapping, primer selection using the 3' Mismatch Rule, and BLAST validation. Includes an automated Python script for candidate primer search.